Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_086509503.1 BZY95_RS08435 acetyl-CoA C-acyltransferase
Query= SwissProt::Q0KBP1 (394 letters) >NCBI__GCF_002151265.1:WP_086509503.1 Length = 396 Score = 420 bits (1079), Expect = e-122 Identities = 216/390 (55%), Positives = 274/390 (70%), Gaps = 2/390 (0%) Query: 5 VVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPRD 64 VV++ RTAIG+FGGSL +AP ELG + REALARA V + H V+G++I T P+D Sbjct: 6 VVILGSARTAIGSFGGSLAGLAPHELGTVTAREALARAGVEAGAIDHAVYGHIITTGPQD 65 Query: 65 MYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRAP 124 YL R A++ GV A A VNRLCGSG+QAI+SAAQ I+LGD+ +A+ GGAESMSR Sbjct: 66 AYLARHIALDAGVPEGAAAFNVNRLCGSGVQAILSAAQQIVLGDSRLALAGGAESMSRGA 125 Query: 125 YLAPA-ARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALES 183 YL P AR G RMG A + D+ LG L DPF HMGVTAEN+AK + R D ALES Sbjct: 126 YLLPPQARNGLRMGHASVTDLTLGVLSDPFGSGHMGVTAENIAKRCGLEREAIDRFALES 185 Query: 184 HRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGTV 243 H +A+ AI G F++QIVPV + K + F DEHVR T++D+ +L+P F KE G V Sbjct: 186 HHKAARAIAEGRFEEQIVPVTVREGKNERQFARDEHVRDGVTLEDLARLKPAFAKE-GVV 244 Query: 244 TAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIALE 303 TAGNASG+ND AA++V+ EA RRGL P ARL+ AGV+P MG+GP+PA + L+ Sbjct: 245 TAGNASGINDGAASLVLAHADEASRRGLAPRARLICASTAGVEPGLMGLGPIPAVRRCLD 304 Query: 304 RAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVKA 363 AGL ++D+DVIE+NEAFAAQA AV + L ++NPNG + LGHP+GATGA++T+KA Sbjct: 305 EAGLSIADIDVIESNEAFAAQAMAVAQELDFPAERLNPNGGAVGLGHPVGATGAILTIKA 364 Query: 364 LHELNRVQGRYALVTMCIGGGQGIAAIFER 393 L EL R GRY L+T+CIGGGQGIA + ER Sbjct: 365 LAELERTGGRYGLITLCIGGGQGIALLIER 394 Lambda K H 0.318 0.134 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 470 Number of extensions: 22 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 394 Length of database: 396 Length adjustment: 31 Effective length of query: 363 Effective length of database: 365 Effective search space: 132495 Effective search space used: 132495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory